How to reproduce:
1. Open attached project "1287352.zip"
2. Open "SampleScene" Scene
3. In Hierarchy window > Click on "Prefab1"
4. In Inspector window > Click on "Something" component
5. Notice which Prefab gets highlighted
6. Repeat 3-5 steps with "Prefab2" and "Prefab3"
7. Unpack "Prefab1"
8. Repeat 3-5 steps with "Prefab1", "Prefab2" and "Prefab3"
9. Save the Scene
10. Open "New Scene" Scene
11. Open "SampleScene" Scene
12. Repeat 3-4 steps with "Prefab1", "Prefab2" and "Prefab3"
13. Notice which things get highlighted

Expected result: Consistency before and after saving the Scene. "Prefab Pointer" referring to Prefabs in the same location.
Actual result: "Something" component in "Prefab Pointer" is referring to Prefabs in the Scene before saving the Scene. After saving the Scene, "Something" component in "Prefab Pointer" is referring to Prefabs in the Assets folder ("Prefab2" is referring to "Prefab3" and it can't found it in the Assets folder for some reason)

Reproducible with: 2019.4.14f1, 2020.1.13f1, 2020.2.0b11, 2021.1.0a3
Not reproducible with: 2021.1.0a5
Couldn't test with: 2018.4 (couldn't downgrade project)

Note: Highly recommend to watch the attached video, because steps can be quite confusing and they are much more clear in the video